9HJZ | pdb_00009hjz

Crystal structure of human geranylgeranyl diphosphate synthase mutant Y246D

• PDB DOI: https://doi.org/10.2210/pdb9HJZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-02 Released: 2025-06-25 
• Deposition Author(s): Yehia, R., Giladi, M., Haitin, Y.
• Funding Organization(s): Israel Science Foundation, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

A somatic multiple myeloma mutation unravels a mechanism of oligomerization-mediated product inhibition in GGPPS.

Yehia, R., Portasikova, J.M., Mor Yosef, R., Da'adoosh, B., Kadek, A., Man, P., Giladi, M., Haitin, Y.

(2025) FEBS J 292: 5802-5817

• PubMed: 40621901 
• DOI: https://doi.org/10.1111/febs.70181
• Primary Citation Related Structures: 
  9HJS, 9HJZ


• PubMed Abstract: 
  

  Protein prenylation plays a critical role in regulating the cellular localization of small GTPases and is essential for multiple myeloma (MM) pathology. Geranylgeranyl diphosphate synthase (GGPPS), producing a key prenylation moiety, exists in a dimeric or hexameric form, depending on the species. However, the functional significance of this oligomerization remains unclear. Using crystallography, mass spectrometry, and fluorescence spectroscopy, we show that the GGPPS ^R235C mutant-found in the widely studied MM cell line RPMI-8226-exhibits weakened inter-dimer interactions, reduced hexamer stability, and increased apparent substrate affinity and product release kinetics. These effects are even more pronounced in a dimeric mutant, GGPPS ^Y246D , demonstrating that interdimer interactions within the hexamer help stabilize a lid region over the active site, thereby stabilizing product binding in an inhibitory conformation. Together, these findings reveal that hexamerization regulates GGPPS activity through product inhibition and underscore the importance of cell line selection and characterization in drug discovery efforts.

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Organizational Affiliation: 
• Department of Physiology and Pharmacology, Gray Faculty of Medical and Health Sciences, Tel-Aviv University, Israel.
Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.
Department of Biochemistry, Faculty of Science, Charles University, Prague 2, Czech Republic.
BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Israel.
Tel Aviv Sourasky Medical Center, Israel.
Sagol School of Neuroscience, Tel Aviv University, Israel.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 70.97 kDa 
• Atom Count: 4,396 
• Modeled Residue Count: 565 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A, B	307	Homo sapiens	Mutation(s): 2  Gene Names: GGPS1 EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95749 (Homo sapiens) Explore O95749  Go to UniProtKB:  O95749
PHAROS:  O95749 GTEx:  ENSG00000152904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.731	α = 90
b = 192.731	β = 90
c = 97.635	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Yehia, R., Giladi, M., Haitin, Y.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1721/16
Israel Science Foundation	Israel	1653/21
Other private	Israel	ICRF 01214
Other private	Israel	ICRF 19202
Other private	Israel	Israel Cancer Association 20230029
Other private	Israel	Kahn Foundation's Orion project
Other private	Israel	Karl and Leonora Fingerhut Fund for Cancer Research
Other private	Israel	Recanati Foundation

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references